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Scientific publications

2025

  • Páscoa Dos Santos F, Verschure PFMJ. Excitatory-inhibitory homeostasis and bifurcation control in the Wilson-Cowan model of cortical dynamics. PLoS Comput Biol. 21(1):e1012723, doi: 10.1371/journal.pcbi.1012723

2024

  • Geminiani A, Kathrein J, Yegenoglu A, Vogel F, Armendariz M, Ben-Zion Z, Bogdan PA, Covelo J, Diaz Pier M, Grasenick K, Karasenko V, Klijn W, Kokan T, Lupascu CA, Lührs A, Mahfoud T, Özden T, Pedersen JE, Peres L, Reiten I, Simidjievski N, Ulnicane I, van der Vlag M, Zehl L, Saria A, Diaz-Pier S, Passecker J. Interdisciplinary and Collaborative Training in Neuroscience: Insights from the Human Brain Project Education Programme. Neuroinformatics 4:657-678, doi: 10.1007/s12021-024-09682-6
  • Dresbach S, Huber R, Gülban ÖF, Pizzuti A, Trampel R, Ivanov D, Weiskopf N, Goebel R. Characterisation of laminar and vascular spatiotemporal dynamics of CBV and BOLD signals using VASO and ME-GRE at 7T in humans. Imaging Neuroscience 2 1–16, doi: 10.1162/imag_a_00263
  • Rocha RP, Zorzi M, Corbetta M. Role of homeostatic plasticity in critical brain dynamics following focal stroke lesions. Sci Rep. 14(1):31631, doi: 10.1038/s41598-024-80196-6
  • Seyedmirzaei H, Soltani Khaboushan A, Abdolalizadeh A et al. Microstructural alterations of cerebellar peduncles in multiple sclerosis: a diffusion tensor imaging study. Acta Neurol Belg. doi: 10.1007/s13760-024-02675-x
  • Páscoa dos Santos F and Verschure PFMJ (2024) Metastable Dynamics Emerge from Local Excitatory-Inhibitory Homeostasis in the Cortex at Rest, bioRxiv 2024.08.24.609501, doi:10.1101/2024.08.24.609501
  • Rolls ET, Yan X, Deco G, Zhang Y, Jousmaki V, Feng J (2024) A ventromedial visual cortical 'Where' stream to the human hippocampus for spatial scenes revealed with magnetoencephalography. Commun Biol. 7(1):1047, doi:10.1038/s42003-024-06719-z
  • Pochinok I, Stöber TM, Triesch J, Chini M, Hanganu-Opatz IL (2024) A developmental increase of inhibition promotes the emergence of hippocampal ripples. Nat Commun. 15(1):738. doi:10.1038/s41467-024-44983-z.
  • Idesis S, Geli S, Faskowitz J, Vohryzek J, Sanz Perl Y, Pieper F, Galindo-Leon E, Engel AK, Deco G (2024) Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex. PLoS Comput Biol. 20(1):e1011818. doi:10.1371/journal.pcbi.1011818
  • Cancino-Fuentes N, Manasanch A, Covelo J, Suarez-Perez A, Fernandez E, Matsoukis S, Guger C, Illa X, Guimerà-Brunet A, Sanchez-Vives MV (2024) Recording physiological and pathological cortical activity and exogenous electric fields using graphene microtransistor arrays in vitro. Nanoscale 16(2), 664 - 677, doi:10.1039/D3NR03842D
  • Quinn AJ, Atkinson LZ, Gohil C, Kohl O, Pitt J, Zich C, Nobre AC, Woolrich MW The GLM-spectrum: A multilevel framework for spectrum analysis with covariate and confound modelling. Imaging Neuroscience 2:1–26. doi:10.1162/imag_a_00082

2023

  • Chen YN, Kostka JK, Bitzenhofer SH, Hanganu-Opatz IL. Olfactory bulb activity shapes the development of entorhinal-hippocampal coupling and associated cognitive abilities. Curr Biol. 33(20):4353-4366.e5, doi: 10.1016/j.cub.2023.08.072.
  • Guder S, Sadeghi F, Zittel S, Quandt F, Choe CU, Bönstrup M, Cheng B, Thomalla G, Gerloff C, Schulz R. Disability and persistent motor deficits are linked to structural crossed cerebellar diaschisis in chronic stroke. Hum Brain Mapp. Nov;44(16):5336-5345, doi: 10.1002/hbm.26434
  • Verschure PFMJ, Páscoa Dos Santos F, Sharma V. (2023) Redefining stroke rehabilitation: Mobilizing the embodied goal-oriented brain. Curr Opin Neurobiol. 83:102807, doi:10.1016/j.conb.2023.102807
  • Csaky R, van Es MWJ, Jones OP, Woolrich M (2023) Group-level brain decoding with deep learning. Hum Brain Mapp. 44(17):6105-6119., doi:10.1002/hbm.26500
  • Csaky R,  van Es MWJ, Parker Jones O, Woolrich M (2023) Interpretable full-epoch multiclass decoding for M/EEG, bioRxiv, doi:10.1101/2023.03.13.532375
  • Seedat ZA, Rier L, Gascoyne LE, Cook H, Woolrich MW, Quinn AJ, Roberts TPL, Furlong PL, Armstrong C, St Pier K, Mullinger KJ, Marsh ED, Brookes MJ, Gaetz W (2023) Mapping Interictal activity in epilepsy using a hidden Markov model: A magnetoencephalography study. Hum Brain Mapp. 44(1):66-81. doi:10.1002/hbm.26118
  • Vidaurre D, Masaracchia L, Larsen NY, Ruijters LRPT, Alonso S, Ahrends C, Woolrich MW (2023) The Gaussian-Linear Hidden Markov model: a Python package,  arXiv:2312.07151, doi:10.48550/arXiv.2312.07151
  • Masaracchia L, Fredes F, Woolrich MW, Vidaurre D (2023) Dissecting unsupervised learning through hidden Markov modeling in electrophysiological data. J Neurophysiol. 30(2):364-379, doi:10.1152/jn.00054.202
  • Vila-Vidal M, Khawaja M, Carreño M, Roldán P, Rumià J, Donaire A, Deco G, Tauste Campo A (2023) Assessing the coupling between local neural activity and global connectivity fluctuations: Application to human intracranial electroencephalography during a cognitive task. Hum Brain Mapp. 44(3):1173-1192, doi:10.1002/hbm.26150
  • Idesis S, Allegra M, Vohryzek J, Sanz Perl Y, Faskowitz J, Sporns O, Corbetta M, Deco G (2023) A low dimensional embedding of brain dynamics enhances diagnostic accuracy and behavioral prediction in stroke. Sci Rep. 13(1):15698, doi:10.1038/s41598-023-42533-z
  • Deco G, Sanz Perl Y, de la Fuente L, Sitt JD, Yeo BTT, Tagliazucchi E, Kringelbach ML (2023) The arrow of time of brain signals in cognition: Potential intriguing role of parts of the default mode network. Netw Neurosci. 7(3):966-998. doi:10.1162/netn_a_00300
  • Pizzuti A, Huber LR, Gulban OF, Benitez-Andonegui A, Peters J, Goebel R (2023) Imaging the columnar functional organization of human area MT+ to axis-of-motion stimuli using VASO at 7 Tesla. Cereb Cortex. 33(13):8693-8711, doi:10.1093/cercor/bhad151
  • Zhang L, Pini L, Kim D, Shulman GL, Corbetta M (2023) Spontaneous Activity Patterns in Human Attention Networks Code for Hand Movements. J Neurosci. 43(11):1976-1986, doi:10.1523/JNEUROSCI.1601-22.2023
  • Zhang L, Pini L, Corbetta M (2023) Different MRI structural processing methods do not impact functional connectivity computation. Sci Rep. 13(1):8589, doi:10.1038/s41598-023-34645-3
  • Sansone G, Pini L, Salvalaggio A, Gaiola M, Volpin F, Baro V, Padovan M, Anglani M, Facchini S, Chioffi F, Zagonel V, D'Avella D, Denaro L, Lombardi G, Corbetta M (2023) Patterns of gray and white matter functional networks involvement in glioblastoma patients: indirect mapping from clinical MRI scans. Front Neurol. 14:1175576, doi: 10.3389/fneur.2023.1175576
  • Rolls ET, Wirth S, Deco G, Huang CC, Feng J (2023) The human posterior cingulate, retrosplenial, and medial parietal cortex effective connectome, and implications for memory and navigation. Hum Brain Mapp. 44(2):629-655, doi:10.1002/hbm.26089
  • Abdolalizadeh A, Ohadi MAD, Ershadi ASB, Aarabi MH (2023) Graph theoretical approach to brain remodeling in multiple sclerosis. Netw Neurosci. 7(1):148-159, doi: 10.1162/netn_a_00276
  • Nabizadeh F, Aarabi MH (2023) Functional and structural lesion network mapping in neurological and psychiatric disorders: a systematic review. Front Neurol. 14:1100067. doi:10.3389/fneur.2023.1100067
  • Rashidi F, Khanmirzaei MH, Hosseinzadeh F, Kolahchi Z, Jafarimehrabady N, Moghisseh B, Aarabi MH (2023) Cingulum and Uncinate Fasciculus Microstructural Abnormalities in Parkinson’s Disease: A Systematic Review of Diffusion Tensor Imaging Studies. Biology 12(3):475. doi:10.3390/biology12030475
  • Sharma, V., Páscoa dos Santos, F., Verschure, P. F. (2023). Patient-specific modeling for guided rehabilitation of stroke patients: The brainx3 use-case. Frontiers in Neurology, 14. doi:10.3389/fneur.2023.1279875
  • Verschure, P. F. M. J., Páscoa dos Santos, F., Sharma, V. (2023). Redefining stroke rehabilitation: Mobilizing the embodied goal-oriented brain. Current Opinion in Neurobiology, 83, 102807. doi:10.1016/j.conb.2023.102807
  • Páscoa dos Santos, F., Vohryzek, J., Verschure, P. F. (2023). Multiscale effects of excitatory-inhibitory homeostasis in lesioned cortical networks: A computational study. PLOS Computational Biology, 19(7). doi:10.1371/journal.pcbi.1011279
  • Castaldo, F., Páscoa dos Santos, F., Timms, R. C., Cabral, J., Vohryzek, J., Deco, G., Woolrich, M., Friston, K., Verschure, P., Litvak, V. (2023). Multi-modal and multi-model interrogation of large-scale functional brain networks. NeuroImage, 277, 120236. doi:10.1016/j.neuroimage.2023.120236
  • Guder, S., Sadeghi, F., Zittel, S., Quandt, F., Choe, C., Bönstrup, M., Cheng, B., Thomalla, G., Gerloff, C., Schulz, R. (2023) Disability and persistent motor deficits are linked to structural crossed cerebellar diaschisis in chronic stroke. Human Brain Mapping 44, 5336–5345. doi:10.1002/hbm.26434
  • Sadeghi, F., Pötter-Nerger, M., Grimm, K., Gerloff, C., Schulz, R., Zittel, S. (2023) Smaller Cerebellar Lobule VIIb is Associated with Tremor Severity in Parkinson’s Disease. The Cerebellum 2023 1–8. doi:10.1007/S12311-023-01532-6
  • Kaduk, T., Goeke, C., Finger, H., König, P. (2023) Webcam eye tracking close to laboratory standards: Comparing a new webcam-based system and the EyeLink 1000. Behavior Research Methods. doi:10.3758/s13428-023-02237-8

2022

  • Chini M, Pfeffer T, Hanganu-Opatz I. An increase of inhibition drives the developmental decorrelation of neural activity. eLife 11:e78811. doi: 10.7554/eLife.78811
  • Sadeghihassanabadi F, Frey BM, Backhaus W, Choe CU, Zittel S, Schön G, Bönstrup M, Cheng B, Thomalla G, Gerloff C, Schulz R. Structural cerebellar reserve positively influences outcome after severe stroke. Brain Commun. 4(6):fcac203. doi: 10.1093/braincomms/fcac203
  • Vohryzek J, Cabral J, Castaldo F, Sanz-Perl Y, Lord LD, Fernandes HM, Litvak V, Kringelbach ML, Deco G (2022) Dynamic sensitivity analysis: Defining personalised strategies to drive brain state transitions via whole brain modelling. Comput Struct Biotechnol J. 21:335-345, doi:10.1016/j.csbj.2022.11.060
  • Cabral J, Castaldo F, Vohryzek J, Litvak V, Bick C, Lambiotte R, Friston K, Kringelbach ML, Deco G. (2022) Metastable oscillatory modes emerge from synchronization in the brain spacetime connectome. Commun Phys. 5:184, doi:10.1038/s42005-022-00950-y
  • Pervaiz U, Vidaurre D, Gohil C, Smith SM, Woolrich MW (2022) Multi-dynamic modelling reveals strongly time-varying resting fMRI correlations. Med Image Anal. 77:102366. doi:10.1016/j.media.2022.102366
  • Ahrends C, Stevner A, Pervaiz U, Kringelbach ML, Vuust P, Woolrich MW, Vidaurre D (2022) Data and model considerations for estimating time-varying functional connectivity in fMRI. Neuroimage. 252:119026, doi:10.1016/j.neuroimage.2022.119026
  • Higgins C, Vidaurre D, Kolling N, Liu Y, Behrens T, Woolrich M (2022) Spatiotemporally resolved multivariate pattern analysis for M/EEG. Hum Brain Mapp. 43(10):3062-3085., doi:10.1002/hbm.25835
  • Higgins C, van Es MWJ, Quinn AJ, Vidaurre D, Woolrich MW (2022) The relationship between frequency content and representational dynamics in the decoding of neurophysiological data. Neuroimage 260:119462. doi:10.1016/j.neuroimage.2022.119462
  • Cruzat J, Perl YS, Escrichs A, Vohryzek J, Timmermann C, Roseman L, Luppi AI, Ibañez A, Nutt D, Carhart-Harris R, Tagliazucchi E, Deco G, Kringelbach ML (2022) Effects of classic psychedelic drugs on turbulent signatures in brain dynamics. Netw Neurosci. 6(4):1104-1124. doi:10.1162/netn_a_00250
  • Rolls ET, Deco G, Huang CC, Feng J (2022) The human language effective connectome. Neuroimage, 258:119352, doi:10.1016/j.neuroimage.2022.119352
  • Formozov A, Chini M, Dieter A, Yang W, Pöpplau JA, Hanganu-Opatz IL, Wiegert JS (2022) Calcium Imaging and Electrophysiology of hippocampal Activity under Anesthesia and natural Sleep in Mice. Sci Data. 9(1):113, doi:10.1038/s41597-022-01244-2
  • Luppi AI, Cabral J, Cofre R, Destexhe A, Deco G, Kringelbach ML (2022) Dynamical models to evaluate structure-function relationships in network neuroscience. Nat Rev Neurosci. 23(12):767-768, doi:10.1038/s41583-022-00646-w
  • Chini M, Pfeffer T, Hanganu-Opatz (2022) An increase of inhibition drives the developmental decorrelation of neural activity, eLife 11:e78811, doi:10.7554/eLife.78811
  • Idesis S, Faskowitz J, Betzel RF, Corbetta M, Sporns O, Deco G (2022) Edge-centric analysis of stroke patients: An alternative approach for biomarkers of lesion recovery. Neuroimage Clin. 35:103055, doi: 0.1016/j.nicl.2022.103055
  • Schepanski S, Chini M, Sternemann V, Urbschat C, Thiele K, Sun T, Zhao Y, Poburski M, Woestemeier A, Thieme MT, Zazara DE, Alawi M, Fischer N, Heeren J, Vladimirov N, Woehler A, Puelles VG, Bonn S, Gagliani N, Hanganu-Opatz IL, Arck PC (2022) Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice. Nat Commun. 13(1):4571, doi:10.1038/s41467-022-32230-2
  • Idesis S, Favaretto C, Metcalf NV, Griffis JC, Shulman GL, Corbetta M, Deco G (2022) Inferring the dynamical effects of stroke lesions through whole-brain modeling. Neuroimage Clin. 36:103233 doi: 10.1016/j.nicl.2022.103233 
  • Cattarinussi G, Moghaddam HS, Aarabi MH, Squarcina L, Sambataro F, Brambilla P, Delvecchio G (2022) White Matter Microstructure Associated with the Antidepressant Effects of Deep Brain Stimulation in Treatment-Resistant Depression: A Review of Diffusion Tensor Imaging Studies. Int J Mol Sci. 23(23):15379. doi: 10.3390/ijms232315379
  • Sadeghihassanabadi, F., Frey, B.M., Backhaus, W., Choe, C., Zittel, S., Schön, G., Bönstrup, M., Cheng, B., Thomalla, G., Gerloff, C., Schulz, R. (2022) Structural cerebellar reserve positively influences outcome after severe stroke. Brain Communications 4, fcac203. doi:10.1093/braincomms/fcac203
  • Sadeghihassanabadi, F., Misselhorn, J., Gerloff, C., Zittel-Dirks, S. (2022). Optimizing the Montage for Cerebellar Transcranial Alternating Current Stimulation (tACS): a Combined Computational and Experimental Study. Journal of Neural Engineering 19(2):026060. doi:10.1088/1741-2552/ac676f
  • Páscoa Dos Santos, F., & Verschure, P. F. (2022) Excitatory-Inhibitory Homeostasis and Diaschisis: Tying the Local and Global Scales in the Post-Stroke Cortex. Frontiers in Systems Neuroscience 15, 161. doi:10.3389/fnsys.2021.806544

2021

  • Sanz Perl Y, Pallavicini C, Pérez Ipiña I, Demertzi A, Bonhomme V, Martial C, Panda R, Annen J, Ibañez A, Kringelbach M, Deco G, Laufs H, Sitt J, Laureys S, Tagliazucchi E (2021) Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness. PLoS Comput Biol. 17(7):e1009139, doi:10.1371/journal.pcbi.1009139
  • Deco G, Kringelbach ML, Arnatkeviciute A, Oldham S, Sabaroedin K, Rogasch NC, Aquino KM, Fornito A (2021) Dynamical consequences of regional heterogeneity in the brain's transcriptional landscape. Sci Adv. 7(29):eabf4752, doi:10.1126/sciadv.abf4752
  • Glomb K, Kringelbach ML, Deco G, Hagmann P, Pearson J, Atasoy S (2021) Functional harmonics reveal multi-dimensional basis functions underlying cortical organization. Cell Rep. 6(8):109554, doi:10.1016/j.celrep.2021.109554
  • Deco G, Perl YS, Sitt JD, Tagliazucchi E, Kringelbach ML (2021) Deep learning the arrow of time in brain activity: characterising brain-environment behavioural interactions in health and disease, bioRxiv 2021.07.02.450899, doi:10.1101/2021.07.02.450899
  • Xu X, Song L, Kringel R, Hanganu-Opatz IL (2021) Developmental decrease of entorhinal-hippocampal communication in immune-challenged DISC1 knockdown mice. Nat Commun. 12(1):6810. doi:10.1038/s41467-021-27114-w
  • Deco G, Sanz Perl Y, Vuust P, Tagliazucchi E, Kennedy H, Kringelbach ML (2021) Rare long-range cortical connections enhance human information processing. Curr Biol. 31(20):4436-4448.e5, doi:10.1016/j.cub.2021.07.064
  • Ódor G, Kelling J, Gastner M, Deco G (2021) Modelling on the very large-scale connectome. Journal of Physics: Complexity 2(4): 045002 doi: 10.1088/2632-072X/ac266c
  • Jancke D, Herlitze S, Kringelbach ML, Deco G (2021) Bridging the gap between single receptor type activity and whole-brain dynamics, The FEBS Journal, doi: 10.1111/febs.15855
  • Grillner S and Thompson WS (2021). Basal ganglia reign through downstream control of motor centers in midbrain and brain stem while updating cortex with efference copy information. Neuron, 109(10), 1587-1589. doi:10.1016/j.neuron.2021.04.015
  • Quinn AJ, Lopes-dos-Santos V, Huang N, Liang W-K, Juan C-h, Yeh J-R, Nobre AC, Dupret D, Woolrich MW (2021). Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics. Journal of Neurophysiology, 126:1190 – 1208. doi:10.1152/jn.00201.2021
  • Quinn AJ, Lopes-dos-Santos V, Dupret D, Nobre AC, Woolrich MW (2021) EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python. Journal of Open Source Software. 6(59):2977. doi:10.21105/joss.02977

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